The 23-year-old pacer did it in 51 matches, overtaking Mitchell Starc who achieved the feat in 52 outings.
Fastest to 100 ODI wickets among fast bowlers (matches)
51 – Shaheen Shah Afridi
52 – Mitchell Starc
54 – Shane Bond
54 – Mustafizur Rahman
55 – Brett Lee
Shaheen is also the fastest Pakistani bowler to reach 100 wickets, going past Saqlain Mushtaq who did it in 53 matches.
Shaheen is considered one of the best bowlers in the world. He features for Pakistan team in all formats of the game and is considered extremely dangerous with the new ball in his hand.
Shaheen made his international debut in Tests, ODIs and T20Is in 2018.
Earlier, Bangladesh captain Shakib Al Hasan won the toss and opted to bat against Pakistan in a crucial World Cup clash.
Bangladesh, who have lost five of their six matches, brought batsman Towhid Hridoy back in for Mahedi Hasan from the side that lost to the Netherlands.
Pakistan have made three changes from the side that lost to South Africa in Chennai by one wicket, recalling fit-again opener Fakhar Zaman as well as Agha Salman and Usama Mir.